The following institutions have significant collections of Thomas Jefferson and Jefferson family manuscripts; they are listed in order of size of their collections.
Library of Congress
- Collection Title: Thomas Jefferson Papers, 1606-1827
- Collection Size: ca. 27,000 items
- Guide: Finding Aid (this refers to the microfilm edition)
- Provenance: The bulk of this collection was sold to the Library of Congress in 1848 by Thomas Jefferson's grandson and executor of his estate, Thomas Jefferson Randolph.
- Items of Interest: Jefferson's copies of the Records of the Virginia Company of London; housekeeping books of his wife, Martha Wayles Skelton Jefferson; weather records;
- Access: Most of this collection has been scanned from the microfilm and is available through the Library of Congress's American Memory project.
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Massachusetts Historical Society
- Collection Title: Coolidge Collection of Thomas Jefferson Manuscripts, 1705-1827
- Collection Size: ca. 9,500 items
- Guide: Finding Aid
- Provenance: Given in four different gifts by Jefferson descendants in 1898, 1911, 1937 and 1957
- Items of Interest: ca. 440 architectural drawings; weather records; portions of Jefferson's account books; his Garden and Farm books; and the manuscript of Notes on the State of Virginia.
- Access: Some of the highlights of this collection have been scanned in color and are available through the Massachusetts Historical Society's website, Thomas Jefferson Papers: An Electronic Archive. The collection is also available on 16 reels of microfilm.

University of Virginia
Collection Title: The Thomas Jefferson Papers
Collection Size: ca. 3,650 items
Guide: See the University's web page for the collection; the entire finding aid (refers to the microfilm edition), which lists each item in the collection, is also available online.
Provenance: Multiple donations from Jefferson himself, family members, and others. More than a third of the collection was donated by descendants in the mid-twentieth century.
Items of Interest: Approximately 80 architectural drawings;
Access: Images of some of the architectural drawings from this collection are available online. The entire collection is available on 10 reels of microfilm.
Missouri History Museum
Collection Title: Thomas Jefferson Collection, 1773-1826
Collection Size: 890 items
Guide: Finding Aid (540KB PDF)
Provenance: Most of the items were donated to the Missouri Historical Society (now the Missouri History Museum) in the early twentieth century by collector William K. Bixby.
Items of Interest: The collection consists mostly of correspondence from Jefferson's presidential years (1801-1809).
Access: The collection is available on 2 reels of microfilm.
- Collection Size: ca. 300 items
- Access: All items from this collection have been scanned in color; images and transcriptions are available online through the Gilder-Lehrman Institute's website.

Gilder-Lehrman Institute (on deposit at the New-York Historical Society)
American Philosophical Society
- Collection Title: Thomas Jefferson Papers, 1775-1825
- Collection Size: ca. 250 items
- Guide: Finding Aid
- Provenance: Presented to APS by Edwin Morris Betts in 1954.
- Access: Some of this collection is available on microfilm (4 reels). Selected items from this collection have been digitized. Links are provided within the online finding aid.
- Collection Title: Thomas Jefferson, letters to and from various persons, 1791-1840
- Collection Size: 63 items
- Guide: Finding Aid
- Access: Items are available on-site only.
- Items of Interest: This collection consists in large part of Jefferson's correspondence with Louis Hue Girardin, regarding Girardin's work on the fourth volume of The History of Virginia (1816).

College of William and Mary
- Collection Title: Thomas Jefferson Papers, 1761-1931
- Collection Size: 160 items
- Guide: Finding Aid
- Provenance: Donated in 1930 by a descendant of William Short's brother.
- Items of Interest: Consists mostly of correspondence between Jefferson and William Short, his personal secretary and protégé.
- Access: All items in this collection have been scanned in color and are available through the library's online catalog. For instructions on accessing these items online, see instructions on the page linked above.
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New York Public Library
Collection Title: Thomas Jefferson Papers, 1765-1826
Collection Size: ca. 65 items
Guide: A finding aid is available on-site. The catalog record for this collection provides a brief description of the contents.
Items of Interest: Jefferson's account book for 1791-1803.
Access: Items are available on-site only.
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Virginia Historical Society
Collection Title: Thomas Jefferson Papers, 1780-1826
Collection Size: 52 items
Guide: Items are individually cataloged and information about them is available through VHS's online catalog (browse for call number Mss2 J3595).
Collection Title: Thomas Jefferson Papers, 1810-1817
Collection Size: 32 items
Guide: Items are individually cataloged and information about them is available through VHS's online catalog (browse for call number Mss2 J3595 b).
